Colon/Rectal Adenocarcinoma: Clustering of Methylation: consensus NMF
Maintained by Robert Zupko
(Broad Institute)
Overview
Introduction
Summary
The 1100 most variable methylated genes were selected based on variation. The variation cutoff are set for each tumor type empirically by fitting a bimodal distriution. For genes with multiple methylation probes, we chose the most variable one to represent the gene. Consensus NMF clustering of 236 samples and 1100 genes identified 2 subtypes with the stability of the clustering increasing for k = 2 to k = 8 and the average silhouette width calculation for selecting the robust clusters.
Results
Silhouette width of each sample in robust cluster
Gene methylation patterns of molecular subtype
Consensus and correlation matrix
Samples assignment with silhouette width
Marker genes of each subtype
Methods & Data
Copyright © 2011
Broad Institute TCGA GDAC as part of the TCGA Research Network.
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